Separation 1: By Former Patron.
Those who have any disease that we can't immediately recognize are to be quarantined carefully, and killed if they show any hostility, with the body burned and purified, as it might carry some strange and horrifying exception to fundamental medical reality. Similarly, we should keep in mind that those who worship Rot are different than those who worship Slaughter or Excess, and each needs to be kept away from 'triggers' and regarded as a risk for these reasons. Those captured who are soldiers are to be considered Prisoners of War of High Danger, and even those who are not are to be considered carefully... though even the worst prisoner is to have food and medical care until or unless it is decided that they are to be executed by firing squad.
Separation 2: By Task Or Deed.
Those who fought in the name of Chaos or who were especially eager for slaughter must be separated from either the reluctant or those who were fundamentally not important.
Separation 3: Among Them.
It is the case that if you have 500 sinners in one community, you have a community of sinners. Instead, for those who willingly surrendered and have not been found to have committed the most vile deeds, we will create Repentance Communities, places where those who wish to redeem the lost and make them Found again. By mixing the faithful and the faithless and creating a model Star Child town, complete with plenty of chapels... and yet also having it being guarded by the fiercely faithful against subversion, we can give these people a taste of the Federation life: food, medical care, houses and all other Quality of Life amenities equal to that of any citizen of the Federation. To those who were captured or who did greater evils, we must keep them spread out. That is to say, a Repentance Community might have 200 such Chaos people and as many or more good Glimmering Federation Citizens devoted to the cause, and especially to be created and encouraged are Orders of Repentance that can peacefully help run these areas, and that can be trusted to provide lists of the devout and the devoted to further people them thus that each sinner lives in a community filled with Faith. But those who either went too far (but not so far as to be executed) or who had to be captured should be held such that there are no more than a dozen at any location, the better to individually monitor them.
-Addendum: Let it be known that those of each of the false Chaos Gods have different needs, and as you might be careful drinking around those who have challenges with alcohol, so too should the communities be made and run with the awareness of what might tempt one, but not another...
Separation 4: Separation By Inquisition.
Those left over, those who fall into the cracks, are to be investigated and tried. Those found too guilty or too corrupted are to be executed, but if there is a chance to save them without granting dishonor to their victims, it must be investigated. Therefore, the Orders and groups involved in this Inquisition must come not only from those preaching Mercy or Justice but also from those who believe in both.
Separation 5: Time.
Conversion can be forced and may have to be, but it also takes time for Faith to take root in the heart. At the end of each year, those in all of the categories are to be evaluated, those doing well and Finding Faith potentially to be moved up, those who are backsliding to be pulled away such that they cannot help others backslide, with the ultimate goal that all who can be saved... and who are WILLING to be saved, will one day be full-citizens released from the Repentance Communities.
-Caveat/Note: The well-being of those who care for, imprison, or judge these people is essential. They are to have regular mental health check-ins with uninvolved people (as well as medical check-ins, considering the risk of disease) and are to be rotated out of their duties every so often as best as possible.